diff --git a/exploration/GR3D_Rdescription/GR3Dmetapopulation.R b/exploration/GR3D_Rdescription/GR3Dmetapopulation.R
new file mode 100644
index 0000000000000000000000000000000000000000..cd1dbe14251d668fe6a760618649a1ac750ab9d8
--- /dev/null
+++ b/exploration/GR3D_Rdescription/GR3Dmetapopulation.R
@@ -0,0 +1,101 @@
+
+#=============================================================================================================
+# metapopulation identification
+# =============================================================================================================
+computeAutochtonousRate = function(data){
+ data %>% filter(migrationBasin == originBasin) %>%
+ select(-originBasin) %>%
+ inner_join(data %>% group_by(year, migrationBasin) %>%
+ summarise(totalRun = sum(effective), .groups = 'drop'), by = c('migrationBasin', 'year')) %>%
+ mutate(autochtonousRate = effective / totalRun) %>%
+ select(year, migrationBasin, autochtonousRate)
+}
+
+computeHomingRate = function(data){
+ data %>% filter(migrationBasin == originBasin) %>%
+ select(-migrationBasin) %>%
+ inner_join(data %>% group_by(year, originBasin) %>%
+ summarise(production = sum(effective), .groups = 'drop'), by = c('originBasin', 'year')) %>%
+ mutate(homingRate = effective / production) %>%
+ select(year, originBasin, homingRate)
+}
+
+# comparison between autochtonous rate and homing rate
+# computeAutochtonousRate(exchangesData) %>%
+# inner_join(computeHomingRate(data = exchangesData), by = c('migrationBasin' = 'originBasin', 'year'))
+
+
+
+identyMetapopulation = function(exchangesData, threshold = .95, verbose = FALSE) {
+ # exchangesData {year, migrationBasin, originBasin)}
+
+ exchangesDataUpdated = exchangesData
+
+ # initialise the connection table between basin and metapopulation
+ metapopulation = exchangesDataUpdated %>%
+ distinct(year, basin = migrationBasin) %>%
+ mutate(metapop = basin)
+
+ iteration = 1
+
+ # find the basin with the minimum autochtonous rate for the first time,
+ basinWithMinAutochtonousRate = computeAutochtonousRate(data = exchangesDataUpdated) %>%
+ group_by(year) %>%
+ slice(which.min(autochtonousRate))
+
+ # loop while autochtonousRate is still < 0.95
+
+ while (basinWithMinAutochtonousRate$autochtonousRate < threshold ) {
+ # while (iteration <= 4 ) {
+ if (verbose) cat(iteration, ": ", basinWithMinAutochtonousRate$autochtonousRate, '\n' )
+
+ # basinWithMinAutochtonousRate will be merged with origin basin sending the maximum number of fish in this basin
+ metapopsToBeMerged <- exchangesDataUpdated %>%
+ inner_join(basinWithMinAutochtonousRate %>% select(-autochtonousRate),
+ by = c('year', 'migrationBasin' )) %>%
+ filter(migrationBasin != originBasin) %>% # to avoid self merging
+ group_by(year) %>%
+ slice(which.max(effective)) %>%
+ ungroup() %>%
+ select(year, migrationBasin, originBasin)
+
+ # update the connection table between basin and metapopulation by merging metapopulation
+ for (i in 1:nrow(metapopsToBeMerged)) {
+ mergedName = paste0("M", iteration, '_',i)
+ metapopsToBeMerged_i <- metapopsToBeMerged %>% slice(i)
+ if (verbose) cat("\t", metapopsToBeMerged_i$migrationBasin, ' + ', metapopsToBeMerged_i$originBasin, ' = ', mergedName, "\n")
+
+ metapopulation <- metapopulation %>%
+ mutate(metapop = if_else(year == metapopsToBeMerged_i$year &
+ metapop %in% (metapopsToBeMerged_i %>% select(ends_with("Basin")) %>% unlist(use.names = FALSE)),
+ mergedName,
+ metapop))
+ }
+ # sum by migration and origin basins according to updated metapopulations
+ # computed with initial exchangesData
+ exchangesDataUpdated <- exchangesData %>%
+ #sum up on migration basins
+ inner_join(metapopulation,
+ by = c('year', 'migrationBasin' = 'basin')) %>%
+ group_by(year, metapop, originBasin) %>%
+ summarise(effective = sum(effective), .groups = 'drop') %>%
+ rename(migrationBasin = metapop) %>%
+ # sum on origine basins
+ inner_join(metapopulation,
+ by = c('year', 'originBasin' = 'basin')) %>%
+ group_by(year, metapop, migrationBasin) %>%
+ summarise(effective = sum(effective), .groups = 'drop') %>%
+ rename(originBasin = metapop)
+
+ # minimum of autochtonous rate
+ basinWithMinAutochtonousRate = computeAutochtonousRate(data = exchangesDataUpdated) %>%
+ group_by(year) %>%
+ slice(which.min(autochtonousRate))
+
+ iteration = iteration + 1
+ }
+ return(list(metapopulation = metapopulation, exchangesData = exchangesDataUpdated))
+}
+
+
+
diff --git a/exploration/GR3D_Rdescription/thermalRanges.R b/exploration/GR3D_Rdescription/thermalRanges.R
new file mode 100644
index 0000000000000000000000000000000000000000..cf5d758f1293a4138f5a282ba81361ce7fbab178
--- /dev/null
+++ b/exploration/GR3D_Rdescription/thermalRanges.R
@@ -0,0 +1,17 @@
+library(tidyverse)
+
+#TODO extract from xml
+
+thermalRange = tibble(process = "Grow", Tmin = 1.7, Topt = 4.5, Tmax = 27.9, type = "Rosso") %>%
+ bind_rows(tibble(process = "SurvivalSpawnerInRiv", Tmin = 5.4, Topt = 16.7, Tmax = 27.5, type = "Rosso") ) %>%
+ bind_rows(tibble(process = "Reproduction", Tmin = 5.1, Topt = 13.5, Tmax = 24.5, type = "Rosso") ) %>%
+ bind_rows(tibble(process = "SurviveAfterReproduction", Tmin = -Inf, Topt = 19.58 - log(19)/0.58, Tmax = 19.58 + log(19)/0.58, type = "logit") )
+
+
+thermalRange %>% mutate(numero = row_number(),
+ process = factor(process,
+ levels = c("Grow","SurvivalSpawnerInRiv", "SurviveAfterReproduction", "Reproduction" ))) %>%
+ ggplot() +
+ geom_segment(aes(x = Tmin, y = process, xend = Tmax, yend = process)) +
+ geom_point(aes(x = Topt, y = process))
+
diff --git a/exploration/NEA_sensitivity_analysis/extractNumeroProcess.R b/exploration/NEA_sensitivity_analysis/extractNumeroProcess.R
index 6d6e57d9e7678f890b6bbc00a1c1384ad50c6485..80bd310c0ba9bfc3ffd044c6c2ada6c667002b25 100644
--- a/exploration/NEA_sensitivity_analysis/extractNumeroProcess.R
+++ b/exploration/NEA_sensitivity_analysis/extractNumeroProcess.R
@@ -1,4 +1,5 @@
library(tidyverse)
+library(XML)
#source("../GR3D_Rdescription/GR3D_NEA_XML_parameters.R")
setwd("~/Documents/workspace/GR3D/exploration/NEA_sensitivity_analysis")
diff --git a/exploration/NEA_sensitivity_analysis/metapopulationIdentification.R b/exploration/NEA_sensitivity_analysis/metapopulationIdentification.R
index 61ddeb400ff91bf41b8badc9f4859fe62288aaee..03b1c22efb62721f7255a9082822393dade46e3e 100644
--- a/exploration/NEA_sensitivity_analysis/metapopulationIdentification.R
+++ b/exploration/NEA_sensitivity_analysis/metapopulationIdentification.R
@@ -1,102 +1,11 @@
-library(tidyverse)
-
-computeAutochtonousRate = function(data){
- data %>% filter(migrationBasin == originBasin) %>%
- select(-originBasin) %>%
- inner_join(data %>% group_by(year, migrationBasin) %>%
- summarise(totalRun = sum(effective), .groups = 'drop'), by = c('migrationBasin', 'year')) %>%
- mutate(autochtonousRate = effective / totalRun) %>%
- select(year, migrationBasin, autochtonousRate)
-}
-
-computeHomingRate = function(data){
- data %>% filter(migrationBasin == originBasin) %>%
- select(-migrationBasin) %>%
- inner_join(data %>% group_by(year, originBasin) %>%
- summarise(production = sum(effective), .groups = 'drop'), by = c('originBasin', 'year')) %>%
- mutate(homingRate = effective / production) %>%
- select(year, originBasin, homingRate)
-}
-
-# comparison between autochtonous rate and homing rate
-# computeAutochtonousRate(exchangesData) %>%
-# inner_join(computeHomingRate(data = exchangesData), by = c('migrationBasin' = 'originBasin', 'year'))
-
-
-
-identyMetapopulation = function(exchangesData, threshold = .95, verbose = FALSE) {
- exchangesDataUpdated = exchangesData
-
- # initialise the connection table between basin and metapopulation
- metapopulation = exchangesDataUpdated %>%
- distinct(year, basin = migrationBasin) %>%
- mutate(metapop = basin)
-
- iteration = 1
-
- # find the basin with the minimum autochtonous rate for the first time,
- basinWithMinAutochtonousRate = computeAutochtonousRate(data = exchangesDataUpdated) %>%
- group_by(year) %>%
- slice(which.min(autochtonousRate))
-
- # loop while autochtonousRate is still < 0.95
-
- while (basinWithMinAutochtonousRate$autochtonousRate < threshold ) {
- # while (iteration <= 4 ) {
- if (verbose) cat(iteration, ": ", basinWithMinAutochtonousRate$autochtonousRate, '\n' )
-
- # basinWithMinAutochtonousRate will be merged with origin basin sending the maximum number of fish in this basin
- metapopsToBeMerged <- exchangesDataUpdated %>%
- inner_join(basinWithMinAutochtonousRate %>% select(-autochtonousRate),
- by = c('year', 'migrationBasin' )) %>%
- filter(migrationBasin != originBasin) %>% # to avoid self merging
- group_by(year) %>%
- slice(which.max(effective)) %>%
- ungroup() %>%
- select(year, migrationBasin, originBasin)
-
- # update the connection table between basin and metapopulation by merging metapopulation
- for (i in 1:nrow(metapopsToBeMerged)) {
- mergedName = paste0("M", iteration, '_',i)
- metapopsToBeMerged_i <- metapopsToBeMerged %>% slice(i)
- if (verbose) cat("\t", metapopsToBeMerged_i$migrationBasin, ' + ', metapopsToBeMerged_i$originBasin, ' = ', mergedName, "\n")
-
- metapopulation <- metapopulation %>%
- mutate(metapop = if_else(year == metapopsToBeMerged_i$year &
- metapop %in% (metapopsToBeMerged_i %>% select(ends_with("Basin")) %>% unlist(use.names = FALSE)),
- mergedName,
- metapop))
- }
- # sum by migration and origin basins according to updated metapopulations
- # computed with initial exchangesData
- exchangesDataUpdated <- exchangesData %>%
- #sum up on migration basins
- inner_join(metapopulation,
- by = c('year', 'migrationBasin' = 'basin')) %>%
- group_by(year, metapop, originBasin) %>%
- summarise(effective = sum(effective), .groups = 'drop') %>%
- rename(migrationBasin = metapop) %>%
- # sum on origine basins
- inner_join(metapopulation,
- by = c('year', 'originBasin' = 'basin')) %>%
- group_by(year, metapop, migrationBasin) %>%
- summarise(effective = sum(effective), .groups = 'drop') %>%
- rename(originBasin = metapop)
-
- # minimum of autochtonous rate
- basinWithMinAutochtonousRate = computeAutochtonousRate(data = exchangesDataUpdated) %>%
- group_by(year) %>%
- slice(which.min(autochtonousRate))
-
- iteration = iteration + 1
- }
- return(list(metapopulation = metapopulation, exchangesData = exchangesDataUpdated))
-}
+require(tidyverse)
+source(GR3Dmetapopulation)
# upload data =====
# longer table of effective of different origin basins in each migration basin
exchangesData <- read_csv("../../data/output/northeastamerica/effectiveFluxes_1-observed.csv")
+
exchangesData %>% group_by(year, basin = originBasin) %>%
summarise(production = sum(effective), .groups = 'drop') %>%
inner_join(exchangesData %>% group_by(year, basin = migrationBasin) %>%
diff --git a/exploration/NEA_sensitivity_analysis/tryFromJava.R b/exploration/NEA_sensitivity_analysis/tryFromJava.R
index a47b94dedc2b72a1aa5feae142ea4c9596f71862..1a4a7b1648f75ccf275c6f5c987624763ffc8b0d 100644
--- a/exploration/NEA_sensitivity_analysis/tryFromJava.R
+++ b/exploration/NEA_sensitivity_analysis/tryFromJava.R
@@ -3,15 +3,16 @@ library(rJava) # see J4R
#library(yaml)
library(tidyverse)
library(jdx)
+library(tictoc)
-rm(list = ls())
+rm(list = ls())
## to have the same working directory as GR3D
#setwd("~/Documents/workspace/GR3D/exploration/NEA_sensitivity_analysis")
setwd("../..")
-
+source("exploration/GR3D_Rdescription/GR3Dmetapopulation.R")
# ====================================== LOCAL FUNCTIONS =====================================
convertFromSALtoR = function(java_out){
require(jdx)
@@ -22,8 +23,8 @@ convertFromSALtoR = function(java_out){
R_out = lapply(seq(2, length(java_out)), FUN = function(i){convertToR(java_out[[i]])}) %>%
unlist() %>%
matrix(nrow = length(java_out) - 1, byrow = TRUE, dimnames = list(NULL, headers) ) %>%
- data.frame() %>%
- suppressMessages(type_convert())
+ as_tibble() %>%
+ type_convert()
return(R_out)
}
@@ -41,7 +42,7 @@ exploreEasyRun = function(){
# 1. northernmost populated basin_id
# 2. centroid latitude
out_range = .jcall("analysis.EasyRun","[[Ljava/lang/String;","getValuesFromAquanismGroupProcess","processes.processesEachStep.10.exportToR")
- range = convertFromSALtoR(out_range)
+ range = suppressMessages(convertFromSALtoR(out_range))
# 3. log-likelihood ----
# the proportion of reproductions leading to a recruitment > 50 over the 1920-1950 period was used
@@ -55,66 +56,79 @@ exploreEasyRun = function(){
# then in R: annual slope of the linear regression
# and average over the period
# 5. mean age of female and age
- # annual mean age in each basin,
- # then in R: average per year,
- # and average over the period (1920 and 1950)
+ # annual mean age over the period (1920 and 1950) in each basin,
+ # and average over basin
out_spawners_features = .jcall("analysis.EasyRun","[[Ljava/lang/String;","getValuesFromAquanismGroupProcess","processes.processesEachStep.9.exportToR")
- spawners_features = convertFromSALtoR(out_spawners_features)
+ spawners_features =suppressMessages (convertFromSALtoR(out_spawners_features))
- ## ICI coder pente de la droite moyenne des ages
+ slopePrimiparous = lm(pct_primiparous~latitude, data = spawners_features)$coeff[2]
+ meanAgeFemale = mean(spawners_features$mean_age_female, na.rm = TRUE)
+ meanAgeMale = mean(spawners_features$mean_age_male, na.rm = TRUE)
# ------------------------------------------------------------ #
# 5. number of metapopulation based on the exchange matrix ----
# mean annual exchange matrix between 1920 and 1950
out_exchanges = .jcall("analysis.EasyRun","[[Ljava/lang/String;","getValuesFromAquanismGroupProcess","processes.processesEachStep.16.exportToR")
- exchanges = convertFromSALtoR(out_exchanges)
+ exchanges = suppressMessages(convertFromSALtoR(out_exchanges))
+
+ # keep only basin with a totalRun (sum over migrationBasin) >0
+ selectedBasin <- exchanges %>% group_by(basin = migrationBasin) %>%
+ summarise(totalRun = sum(effective), .groups = 'drop') %>%
+ filter(totalRun > 0) %>% select(basin)
- ## ICI lancer metapopulationIdentification
+ metapopulations <- exchanges %>% inner_join(selectedBasin, by=c('migrationBasin' = 'basin')) %>%
+ inner_join(selectedBasin, by=c('natalBasin' = 'basin')) %>%
+ mutate(year =0) %>% rename(originBasin = natalBasin) %>%
+ identyMetapopulation(., threshold = .95, verbose = FALSE)
+ nbMetapopulation = metapopulations$metapopulation %>%
+ distinct(metapop) %>%
+ summarise(n = n()) %>%
+ unlist(use.names = FALSE)
- return(list(northern_basin_id = range$northern_basin_id,
- effective_centroid_latitude = range$effective_centroid_latitude,
- logL = logL,
- spawners_features = spawners_features,
- exchanges = exchanges))
+ return(tibble(northern_basin_id = range$northern_basin_id,
+ effective_centroid_latitude = range$effective_centroid_latitude,
+ logL = logL,
+ slopePrimiparous = slopePrimiparous,
+ meanAgeFemale = meanAgeFemale,
+ meanAgeMale = meanAgeMale,
+ nbMetapopulation = nbMetapopulation))
}
# GR3D arguments -----------------------------------------
-jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
-simDuration = 150
-simBegin = 1
-timeStepDuration = 1
-
-seed = 1
-#'-q',
-arguments = c('-simDuration', simDuration, '-simBegin',simBegin,
- '-timeStepDuration', timeStepDuration,
- '-RNGStatusIndex', format(seed,scientific = FALSE),
- '-groups',"data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml",
- '-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
- '-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
-
-
-
+#' jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
+#' simDuration = 150
+#' simBegin = 1
+#' timeStepDuration = 1
+#'
+#' seed = 1
+#' #'-q',
+#' arguments = c('-simDuration', simDuration, '-simBegin',simBegin,
+#' '-timeStepDuration', timeStepDuration,
+#' '-RNGStatusIndex', format(seed,scientific = FALSE),
+#' '-groups',"data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml",
+#' '-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
+#' '-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
# -----------------------------------------------------
# initializes the Java Virtual Machine -------------------------------------
+jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
.jinit(NULL, force.init = TRUE)
.jinit(classpath = jarfile, force.init = TRUE)
.jclassPath()
# modification of xlm parameters -----------------------
-parametersNamesANG = c("processes.processesEachStep.11.Soffset")
-thetasANG = c(-1)
-
-parametersNamesENV = c("simulationName")
-thetasENV = c("Allee")
+# parametersNamesANG = c("processes.processesEachStep.11.Soffset")
+# thetasANG = c(-1)
+#
+# parametersNamesENV = c("simulationName")
+# thetasENV = c("Allee")
# run the GR3D with updated parameter values in processes --------------------------------------------
-runEasyRun(arguments, parametersNamesANG,thetasANG, parametersNamesENV, thetasENV )
+# runEasyRun(arguments, parametersNamesANG,thetasANG, parametersNamesENV, thetasENV )
# .jcall("analysis.EasyRun", "V", "runSimulation", arguments,
# .jarray(parametersNamesANG), .jarray(thetasANG),
@@ -122,42 +136,60 @@ runEasyRun(arguments, parametersNamesANG,thetasANG, parametersNamesENV, thetasEN
# call GR3D method to get model outputs ----------------------------------------------
-res1 = exploreEasyRun()
-res1$spawners_features
-#
-listeSimulation <- list(list(replicat = 1,
- parametersNamesANG = c("processes.processesEachStep.11.Soffset"),
- thetasANG = c(-1),
- parametersNamesENV = c("simulationName"),
- thetasENV = c("Allee")),
- list(replicat = 1,
- parametersNamesANG = c("processes.processesEachStep.11.Soffset"),
- thetasANG = c(0),
- parametersNamesENV = c("simulationName"),
- thetasENV = c("no Allee")))
-
-for (i in 1:length(listeSimulation)) {
- arguments = c('-simDuration', simDuration, '-simBegin',simBegin,
- '-timeStepDuration', timeStepDuration,
- '-RNGStatusIndex', format(listeSimulation[[i]]$replicat,scientific = FALSE),
+runSimulation = function(simulationParameter) {
+ arguments = c('-simDuration', 600, '-simBegin',2,
+ '-timeStepDuration', 1,
+ '-RNGStatusIndex', format(simulationParameter$replicat,scientific = FALSE),
'-groups',"data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml",
'-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
'-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
- parametersNamesANG = listeSimulation[[i]]$parametersNamesANG
- thetasANG = listeSimulation[[i]]$thetasANG
- parametersNamesENV = listeSimulation[[i]]$parametersNamesENV
- thetasENV = listeSimulation[[i]]$thetasENV
-
runEasyRun(arguments,
- parametersNamesANG,
- thetasANG,
- parametersNamesENV ,
- thetasENV )
- res1 = exploreEasyRun()
- cat(res1$effective_centroid_latitude, "\n")
+ parametersNamesANG = simulationParameter$parametersNamesANG,
+ thetasANG = simulationParameter$thetasANG,
+ parametersNamesENV = simulationParameter$parametersNamesENV,
+ thetasENV = simulationParameter$thetasENV )
+
+ #tic()
+ result = exploreEasyRun()
+ #toc()
+ return(result)
}
-toto = listeSimulation[[i]]$parametersNamesANG
+
+#============================
+listeSimulation <- list(list(replicat = 1,
+ parametersNamesANG = c("processes.processesEachStep.11.Soffset",
+ "processes.processesEachStep.6.pHomingAfterEquil"),
+ thetasANG = c(-1, 0.97),
+ parametersNamesENV = c("simulationName"),
+ thetasENV = c("Allee_highHoming")),
+
+ list(replicat = 1,
+ parametersNamesANG = c("processes.processesEachStep.11.Soffset",
+ "processes.processesEachStep.6.pHomingAfterEquil"),
+ thetasANG = c(-1, 0.75),
+ parametersNamesENV = c("simulationName"),
+ thetasENV = c("Allee_lowHoming")),
+
+ list(replicat = 1,
+ parametersNamesANG = c("processes.processesEachStep.11.Soffset",
+ "processes.processesEachStep.6.pHomingAfterEquil"),
+ thetasANG = c(0, 0.97),
+ parametersNamesENV = c("simulationName"),
+ thetasENV = c("noAllee_highHoming")),
+
+ list(replicat = 1,
+ parametersNamesANG = c("processes.processesEachStep.11.Soffset",
+ "processes.processesEachStep.6.pHomingAfterEquil"),
+ thetasANG = c(0, 0.75),
+ parametersNamesENV = c("simulationName"),
+ thetasENV = c("noAllee_lowHoming"))
+ )
+tic()
+resSimulation = lapply(listeSimulation, runSimulation)
+toc()
+
+save(listeSimulation, resSimulation, file = 'simulation.Rdata')
diff --git a/src/main/java/analysis/AnalyseFishDistribution.java b/src/main/java/analysis/AnalyseFishDistribution.java
index a1839c52104b209d7d68795514e6f1c1cdf4af3b..dc037c1f0420f50c3449dc537b03ce9e3401ca60 100644
--- a/src/main/java/analysis/AnalyseFishDistribution.java
+++ b/src/main/java/analysis/AnalyseFishDistribution.java
@@ -254,40 +254,34 @@ public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFis
// initialise the distribution range
double southernEdge = northernLimit;
double northernEdge = southernLimit;
- int southernId = -1;
- int northernId = -1;
- String southernName = "";
- String northernName = "";
- // String southernName = "";
- // String northernName = "";
+
+ RiverBasin northernBasin = null;
+ RiverBasin southernBasin = null;
+
// initialise for centroid
TreeMapForCentile latitudeEffective = new TreeMapForCentile();
TreeMapForCentile latitudePresence = new TreeMapForCentile();
- String[][] export = new String[2][6];
-
for (RiverBasin riverBasin : riverBasins) {
double meanLastRecruitment = riverBasin.getLastRecruitments().getMean();
if (meanLastRecruitment >= minimumRecruitsForPopulatedBasin) {
// the river basin is considered populated
- // NOTE : recruiit number is calulated after thermal tolerance impact
+ // CHECK : recruiit number is calulated after thermal tolerance impact
// (which is intreaged in the stock-recruitment relationship)
// southern edge
if (riverBasin.getLatitude() < southernEdge) {
// the basin is the new southern edge
southernEdge = riverBasin.getLatitude();
- southernId = riverBasin.getBasin_id();
- southernName = riverBasin.getName();
+ southernBasin = riverBasin;
}
// northern edge
if (riverBasin.getLatitude() > northernEdge) {
// the basin is the new northern edge
northernEdge = riverBasin.getLatitude();
- northernId = riverBasin.getBasin_id();
- northernName = riverBasin.getName();
+ northernBasin = riverBasin;
}
// for distribution centroide computation
@@ -297,29 +291,41 @@ public class AnalyseFishDistribution extends AquaNismsGroupProcess<DiadromousFis
}
}
- // if the universe is empty (none of basins is populated)
- if (southernEdge == northernLimit & northernEdge == southernLimit) {
- southernEdge = (northernLimit + southernLimit) / 2.;
- northernEdge = southernEdge;
- }
-
// distribution centroids computation
double basinCentroid = latitudePresence.calculateMedian();
double effectiveCentroid = latitudeEffective.calculateMedian();
+ // export
+ String[][] export = new String[2][8];
export[0][0] = "southern_basin_id";
export[0][1] = "southern_basin_name";
- export[0][2] = "northern_basin_id";
- export[0][3] = "northern_basin_name";
- export[0][4] = "basin_centroid_latitude";
- export[0][5] = "effective_centroid_latitude";
-
- export[1][0] = String.valueOf(southernId);
- export[1][1] = southernName;
- export[1][2] = String.valueOf(northernId);
- export[1][3] = northernName;
- export[1][4] = String.valueOf(basinCentroid);
- export[1][5] = String.valueOf(effectiveCentroid);
+ export[0][2] = "southern_latitude";
+ export[0][3] = "northern_basin_id";
+ export[0][4] = "northern_basin_name";
+ export[0][5] = "northern_latitude";
+ export[0][6] = "basin_centroid_latitude";
+ export[0][7] = "effective_centroid_latitude";
+
+ if (southernBasin != null & northernBasin != null) {
+ export[1][0] = String.valueOf(southernBasin.getBasin_id());
+ export[1][1] = southernBasin.getName();
+ export[1][2] = String.valueOf(southernBasin.getLatitude());
+ export[1][3] = String.valueOf(northernBasin.getBasin_id());
+ export[1][4] = northernBasin.getName();
+ export[1][5] = String.valueOf(northernBasin.getLatitude());
+ export[1][6] = String.valueOf(basinCentroid);
+ export[1][7] = String.valueOf(effectiveCentroid);
+ } else {
+ export[1][0] = "NA";
+ export[1][1] = "NA";
+ export[1][2] = "NA";
+ export[1][3] = "NA";
+ export[1][4] = "NA";
+ export[1][5] = "NA";
+ export[1][6] = "NA";
+ export[1][7] = "NA";
+ }
+
return export;
}
diff --git a/src/main/java/analysis/AnalyseSpawnerFeatures.java b/src/main/java/analysis/AnalyseSpawnerFeatures.java
index 79faa13861041368eda95d03c731c40caf842ebe..50c7bc17f66b4dc7f7865a91ac1423253476e234 100644
--- a/src/main/java/analysis/AnalyseSpawnerFeatures.java
+++ b/src/main/java/analysis/AnalyseSpawnerFeatures.java
@@ -328,7 +328,7 @@ public class AnalyseSpawnerFeatures extends AquaNismsGroupProcess<DiadromousFish
result[0][1] = "basin_name";
result[0][2] = "latitude";
result[0][3] = "mean_age_female"; // primiparous and multiparous
- result[0][4] = "mean_age _male"; // primiparous and multiparous
+ result[0][4] = "mean_age_male"; // primiparous and multiparous
result[0][5] = "pct_primiparous";
int i = 1;
diff --git a/src/main/java/analysis/EasyRun.java b/src/main/java/analysis/EasyRun.java
index d528cd319699cc746bb77e276cf80ef4cd2e636b..e4bbbf13fa9b89581e6acbc42fed70baeae6f3f7 100644
--- a/src/main/java/analysis/EasyRun.java
+++ b/src/main/java/analysis/EasyRun.java
@@ -55,7 +55,6 @@ public class EasyRun {
public static void runSimulation(String[] batchArgs, String[] paramNameaANG, double[] paramValuesANG, String[] paramNameaENV,
String[] paramValuesENV) throws Exception {
- // TODO parse string to other type if needed
try {
pilot = new Pilot();
BatchRunner runner = new BatchRunner(pilot);
@@ -129,21 +128,29 @@ public class EasyRun {
// double[] parameterValues = new double[] { 10, 2, 0.7 };
// =====================================================
- System.out.println("WITHOUT ALLEE EFFECT");
- String[] parameterNamesANG = new String[] { "processes.processesEachStep.11.Soffset" };
- double[] parameterValuesANG = new double[] { 0. };
+ // System.out.println("WITHOUT ALLEE EFFECT");
+ // String[] parameterNamesANG = new String[] { "processes.processesEachStep.11.Soffset" };
+ // double[] parameterValuesANG = new double[] { 0. };
+ // // runSimulation(batchArguments, parameterNamesANG, parameterValuesANG);
+ // String[] parameterNamesENV = new String[] { "simulationName" };
+ // String[] parameterValuesENV = new String[] { "noAllee" };
+
+ System.out.println("reference");
+ String[] parameterNamesANG = new String[0];
+ double[] parameterValuesANG = new double[0];
// runSimulation(batchArguments, parameterNamesANG, parameterValuesANG);
- String[] parameterNamesENV = new String[] { "simulationName" };
- String[] parameterValuesENV = new String[] { "noAllee" };
+ String[] parameterNamesENV = new String[0];
+ String[] parameterValuesENV = new String[0];
+
runSimulation(batchArguments, parameterNamesANG, parameterValuesANG, parameterNamesENV, parameterValuesENV);
- System.out.println("\n== AnalyseSpawnerFeatures ==");
- String[][] spawnerRunResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.9.exportToR");
- for (String[] record : spawnerRunResults) {
- for (String value : record)
- System.out.print(value + "\t");
- System.out.println();
- }
+ // System.out.println("\n== AnalyseSpawnerFeatures ==");
+ // String[][] spawnerRunResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.9.exportToR");
+ // for (String[] record : spawnerRunResults) {
+ // for (String value : record)
+ // System.out.print(value + "\t");
+ // System.out.println();
+ // }
System.out.println("\n== AnalyseFishDistribution ==");
String[][] distributionResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.10.exportToR");
@@ -156,13 +163,14 @@ public class EasyRun {
System.out.println("\n== AnalyseLikelihoodOfPresence ==");
System.out.println(getSingleValueFromAquanismGroupProcess("processes.processesAtEnd.0.getLogLikelihood"));
- System.out.println("\n== ExportExchangeSBetweenCatchments ==");
- String[][] exchangeSBetweenCatchments = getValuesFromAquanismGroupProcess("processes.processesEachStep.16.exportToR");
- for (String[] record : exchangeSBetweenCatchments) {
- for (String value : record)
- System.out.print(value + "\t");
- System.out.println();
- }
+ // System.out.println("\n== ExportExchangeSBetweenCatchments ==");
+ // String[][] exchangeSBetweenCatchments =
+ // getValuesFromAquanismGroupProcess("processes.processesEachStep.16.exportToR");
+ // for (String[] record : exchangeSBetweenCatchments) {
+ // for (String value : record)
+ // System.out.print(value + "\t");
+ // System.out.println();
+ // }
}
}
diff --git a/src/main/java/analysis/ExportExchangesBetweenCatchments.java b/src/main/java/analysis/ExportExchangesBetweenCatchments.java
index 88e894f00e53fec00102d0709510b98497138dd0..67efe43a1e8dac913381060e0ed90d32b7ab9749 100644
--- a/src/main/java/analysis/ExportExchangesBetweenCatchments.java
+++ b/src/main/java/analysis/ExportExchangesBetweenCatchments.java
@@ -241,22 +241,17 @@ public class ExportExchangesBetweenCatchments extends AquaNismsGroupProcess<Diad
public String[][] exportToR() {
int i, j;
- String[][] export = new String[riverBasins.length + 1][riverBasins.length + 1];
+ String[][] export = new String[riverBasins.length * riverBasins.length + 1][3];
// headers
export[0][0] = "migrationBasin";
- j = 1;
- for (RiverBasin natalBasin : riverBasins) {
- export[0][j] = natalBasin.getName();
- j++;
- }
-
+ export[0][1] = "natalBasin";
+ export[0][2] = "effective";
i = 1;
for (RiverBasin migrationBasin : riverBasins) {
- export[i][0] = migrationBasin.getName();
- j = 1;
- for (RiverBasin natalBasin : riverBasins) {
+ for (RiverBasin natalBasin : riverBasins) {
+ // compute the mean over years
Map<Long, Double> year_effective = exchanges.get(migrationBasin).get(natalBasin);
int n = 0;
double sum = 0;
@@ -266,10 +261,12 @@ public class ExportExchangesBetweenCatchments extends AquaNismsGroupProcess<Diad
sum += effective;
}
}
- export[i][j] = String.valueOf(Math.round(10. * sum / n) / 10);
- j++;
+ // fill in export array
+ export[i][0] = migrationBasin.getName();
+ export[i][1] = natalBasin.getName();
+ export[i][2] = String.valueOf(Math.round(10. * sum / n) / 10.);
+ i++;
}
- i++;
}
return export;
diff --git a/src/main/java/environment/BasinNetworkObserverPresence.java b/src/main/java/environment/BasinNetworkObserverPresence.java
index 1246c13c568b2a760e1f942ca7aecca0b545990c..4b27f34f7c6af45f96c730d599a8d6d734269111 100644
--- a/src/main/java/environment/BasinNetworkObserverPresence.java
+++ b/src/main/java/environment/BasinNetworkObserverPresence.java
@@ -37,8 +37,7 @@ import fr.cemagref.simaqualife.kernel.util.TransientParameters;
import fr.cemagref.simaqualife.pilot.Pilot;
@SuppressWarnings("serial")
-public class BasinNetworkObserverPresence extends ObserverListener
- implements Configurable, Drawable, MouseMotionListener {
+public class BasinNetworkObserverPresence extends ObserverListener implements Configurable, Drawable, MouseMotionListener {
private String title;
@@ -46,6 +45,8 @@ public class BasinNetworkObserverPresence extends ObserverListener
private String period = "obs_1751_1850";
+ private Boolean fillInshoreBasin = false;
+
@Description(name = "Color scale", tooltip = "")
public ColorScaleEnum colorScaleEnum = ColorScaleEnum.BluesScale;
@@ -73,11 +74,13 @@ public class BasinNetworkObserverPresence extends ObserverListener
// basin under the mouse
private transient Basin basinUnderMouse;
-
@TransientParameters.InitTransientParameters
public void init(Pilot pilot) {
this.pilot = pilot;
+ if (fillInshoreBasin == null)
+ fillInshoreBasin = false;
+
if (this.colorScaleEnum == null) {
this.colorScaleEnum = ColorScaleEnum.RedsScale;
@@ -113,13 +116,13 @@ public class BasinNetworkObserverPresence extends ObserverListener
}
}
}
- // reader.close();
- // scanner.close();
+ reader.close();
+ scanner.close();
} catch (Exception e) {
e.printStackTrace();
}
-
}
+
// the Jpanal that holds all the components to be displayed
display = new JPanel(new BorderLayout());
@@ -142,7 +145,6 @@ public class BasinNetworkObserverPresence extends ObserverListener
}
-
/*
* @Override public void valueChanged(ObservablesHandler arg0, Object arg1, long arg2) {
*
@@ -152,6 +154,7 @@ public class BasinNetworkObserverPresence extends ObserverListener
* label.setText(txt); display.repaint(); }
*/
+
@Override
public void mouseDragged(MouseEvent arg0) {
// nothing to do
@@ -327,12 +330,21 @@ public class BasinNetworkObserverPresence extends ObserverListener
* else g.setColor(Color.LIGHT_GRAY);
*/
- if (presence > 0)
- g.setColor(colorScaleEnum.getScale().getColor(presence));
- else if (presence == 0)
- g.setColor(Color.WHITE);
- else
- g.setColor(Color.GRAY);
+ if (basin instanceof RiverBasin) {
+ if (presence > 0)
+ g.setColor(colorScaleEnum.getScale().getColor(presence));
+ else if (presence == 0)
+ g.setColor(Color.WHITE);
+ else
+ g.setColor(Color.GRAY);
+ } else if (basin instanceof InshoreBasin & fillInshoreBasin) {
+ if (presence > 0)
+ g.setColor(colorScaleEnum.getScale().getColor(presence));
+ else if (presence == 0)
+ g.setColor(Color.WHITE);
+ else
+ g.setColor(Color.GRAY);
+ }
g2d.fill(displayShape);
}
@@ -341,10 +353,9 @@ public class BasinNetworkObserverPresence extends ObserverListener
public enum ColorScaleEnum {
- RedsScale(new RedsScale()), BluesScale(new BluesScale()), BicolorScale(new BicolorScale()), GraysScale(
- new GraysScale());
- private ColorScale scale;
+ RedsScale(new RedsScale()), BluesScale(new BluesScale()), BicolorScale(new BicolorScale()), GraysScale(new GraysScale());
+ private ColorScale scale;
ColorScaleEnum(ColorScale colorScale) {
scale = colorScale;
diff --git a/src/main/java/environment/RIOBasinNetworkObserverPresence.java b/src/main/java/environment/RIOBasinNetworkObserverPresence.java
index f30f81cba30d1c80005eac5badf329f6a91bb210..a51b111c72a4b4f8ce74e7747e96a56696b8e158 100644
--- a/src/main/java/environment/RIOBasinNetworkObserverPresence.java
+++ b/src/main/java/environment/RIOBasinNetworkObserverPresence.java
@@ -45,6 +45,8 @@ public class RIOBasinNetworkObserverPresence extends ObserverListener implements
private String period = "obs_1751_1850";
+ private Boolean fillInshoreBasin = false;
+
@Description(name = "Color scale", tooltip = "")
public ColorScaleEnum colorScaleEnum = ColorScaleEnum.BluesScale;
@@ -72,11 +74,13 @@ public class RIOBasinNetworkObserverPresence extends ObserverListener implements
// basin under the mouse
private transient Basin basinUnderMouse;
-
@TransientParameters.InitTransientParameters
public void init(Pilot pilot) {
this.pilot = pilot;
+ if (fillInshoreBasin == null)
+ fillInshoreBasin = false;
+
if (this.colorScaleEnum == null)
this.colorScaleEnum = ColorScaleEnum.RedsScale;
@@ -139,7 +143,6 @@ public class RIOBasinNetworkObserverPresence extends ObserverListener implements
bn = (RIOBasinNetworkWithContinent) pilot.getAquaticWorld().getEnvironment();
}
-
/*
* @Override public void valueChanged(ObservablesHandler arg0, Object arg1, long arg2) {
*
@@ -149,6 +152,7 @@ public class RIOBasinNetworkObserverPresence extends ObserverListener implements
* label.setText(txt); display.repaint(); }
*/
+
@Override
public void mouseDragged(MouseEvent arg0) {
// nothing to do
@@ -318,12 +322,22 @@ public class RIOBasinNetworkObserverPresence extends ObserverListener implements
else
System.out.println(basinName + " is not present in the presence file");
- if (presence > 0)
- g.setColor(colorScaleEnum.getScale().getColor(presence));
- else if (presence == 0)
- g.setColor(Color.WHITE);
- else
- g.setColor(Color.GRAY);
+ if (basin instanceof RiverBasin) {
+ if (presence > 0)
+ g.setColor(colorScaleEnum.getScale().getColor(presence));
+ else if (presence == 0)
+ g.setColor(Color.WHITE);
+ else
+ g.setColor(Color.GRAY);
+ } else if (basin instanceof InshoreBasin & fillInshoreBasin) {
+ if (presence > 0)
+ g.setColor(colorScaleEnum.getScale().getColor(presence));
+ else if (presence == 0)
+ g.setColor(Color.WHITE);
+ else
+ g.setColor(Color.GRAY);
+ } else
+ g.setColor(Color.BLUE);
g2d.fill(displayShape);
}
@@ -334,8 +348,8 @@ public class RIOBasinNetworkObserverPresence extends ObserverListener implements
public enum ColorScaleEnum {
RedsScale(new RedsScale()), BluesScale(new BluesScale()), BicolorScale(new BicolorScale()), GraysScale(new GraysScale());
- private ColorScale scale;
+ private ColorScale scale;
ColorScaleEnum(ColorScale colorScale) {
scale = colorScale;
diff --git a/src/main/java/species/ReproduceWithDiagnose.java b/src/main/java/species/ReproduceWithDiagnose.java
index e45c074cfc423f068750531bf6244b48ef6009ee..0eb64bb656f71299a894b0ba7c05dfbf174dff72 100644
--- a/src/main/java/species/ReproduceWithDiagnose.java
+++ b/src/main/java/species/ReproduceWithDiagnose.java
@@ -25,7 +25,6 @@ import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
import fr.cemagref.simaqualife.pilot.Pilot;
-import miscellaneous.BinomialForSuperIndividualGen;
import miscellaneous.Miscellaneous;
import miscellaneous.Trio;
import species.DiadromousFish.Gender;
@@ -83,12 +82,12 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
private transient NormalGen genNormal;
- /**
- * the random numbers generator for binomial draws
- *
- * @unit --
- */
- private transient BinomialForSuperIndividualGen aleaGen;
+ // /**
+ // * the random numbers generator for binomial draws
+ // *
+ // * @unit --
+ // */
+ // private transient BinomialForSuperIndividualGen aleaGen;
private transient MortalityFunction mortalityFunction;
@@ -111,7 +110,7 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
super.initTransientParameters(pilot);
genNormal = new NormalGen(pilot.getRandomStream(), new NormalDist(0., 1.));
- aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
+ // aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
mortalityFunction = new MortalityFunction();
stockRecruitmentRelationship = new StockRecruitmentRelationship();
@@ -205,11 +204,11 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
amountPerSuperIndividual = alpha / maxNumberOfSuperIndividualPerReproduction;
// Compute the Allee effect parameters S95 and S50
- if (Soffset >= 0.) {// Allee effect independant of catchment size (including
+ if (Soffset >= 0.) {// Allee effect independant of catchment size (including no Allee Effect)
S95 = Soffset;
S50 = Soffset;
} else {
- S95 = eta * riverBasin.getAccessibleSurface(); // corresponds to S* in the rougier publication
+ S95 = eta * riverBasin.getAccessibleSurface(); // corresponds to S* in the rougier etal 2015
S50 = S95 / ratioS95_S50;
}
// initilisation of the stock recruitment relationship
@@ -535,7 +534,7 @@ class StockRecruitmentRelationship implements UnivariateFunction {
// BH Stock-Recruitment relationship with logistic depensation
double meanNumberOfRecruit = 0.;
double effectiveStock = getEffectiveStock(stock);
- if (stock > 0)
+ if (effectiveStock > 0)
meanNumberOfRecruit = Math.round(alpha * effectiveStock) / (beta + effectiveStock);
return meanNumberOfRecruit;
}